Estrogens exert their regulatory potential on gene expression through different nuclear and non-nuclear mechanisms. A direct nuclear approach is the interaction of estrogen with specific target sequences of DNA, estrogen response elements (ERE) or units. EREs can be grouped into perfect and imperfect palindromic sequences with the imperfect sequences differing from the consensus sequence in one or more nucleotides and being less responsive to the activated estrogen-estrogen receptor (ER) complex. Differences in the ERE sequence and the ER subtype involved can substantially alter ER-ERE interaction. In addition, cross-talk between ERs and other nuclear transcription factors profoundly influences gene expression. Here, we focus on the recent advances in the understanding of the structure of EREs and how ERs are recruited to these. Identifying known target genes for estrogen action could help us to understand the potential risks and benefits of the administration of this steroid to humans.